Abstract
The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.
Highlights
The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood
We find that C. ryukyuensis is related to but genetically distinct from tachibana and shiikuwasha
We find that tachibana is a collection of hybrids between C. ryukyuensis and mainland Asian mandarins, but distinct from shiikuwasha (Fig. 3b, Supplementary Note 5)
Summary
The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. The taxonomic complexity of east Asian mandarins collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We find that the complexity of mandarin relationships is considerably simplified by the discovery of three ancestral lineages which, together with pummelo, gave rise to all extant mandarin diversity by hybridization and introgression One of these groups is a previously unknown wild species currently found in the Ryukyu islands; the other two are previously unrecognized sister subspecies of mainland Asian mandarin. Our analysis leads to a comprehensive revision of the origin and diversification of east Asian citrus, including the elucidation of the origins of apomixis in mandarin and its spread to related citrus including oranges, grapefruits and lemons
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